Elevate research projects with Quarto

MS Víctor Gauto

Dr. Matías Bonansea

ICBIA (UNRC, CONICET)

Dr. Anabella Ferral

Instituto Gulich (UNC, CONAE)

Dr. Osvaldo Cardozo

IIDTHH (UNNE, CONICET)

Dr. Claudia Giardino

IREA (CNR)

2025-03-06

Content

Introduction
Motivation
Tools
Future improvements
Resources

https://vhgauto.quarto.pub/seminario2-gulich/

Introduction

Research project

To estimate water quality indicators in Paraná River middle basin for algorithm development using satellite remote sensing techniques

Collaborative website with automatic running, interactive and open source.

Front page

Authors
Affiliation
Last modified date
Keywords
More resources links

Table of content

Sections and subsections
Ease website navigation
Variable content according to the development

Notebooks

Source code description
Processing data justification
Calculus methodology explanation to promote reproducibility

References

Formatted references according to desired style (.csl)
Reference preview on citation hover

Maps, tables & interactive plots

Results visualization
Correlation between parameters exploration
Spectral properties description
Sample site location

Web site

https://vhgauto.quarto.pub/gistaq-parana/

Motivation

Research project typical life journey.

%%{
  init: {
    'themeVariables': {
      'edgeLabelBackground': '#224289'
    }
  }
}%%

flowchart LR
    a1[Thinking] ==> a2[Beginning]
    a2 ====> |<span class="svg-spinners--clock"></span>| a3[Main goal]

    a3 ==> a4([Paper])
    a3 ==> a5([Conference])
    a3 ==> a6([Report])

Water sampling
Physicochemical test
Partial results analyses
Reference reading
Other tasks

During the project development

Dynamic document, that adapts to the current project state.
Easy access site to check the latest results.
Unified reference search.
Script code execution and results reproducibility.
All project members can work seamless and without problems and no fear of disarranging the document.
Consultation resource and to admire all the effort done.

Tools

R y Python: reading and data collection; processing and results storage; plots, tables and maps generation.
Git y GitHub: version control management and project members collaboration.
Quarto: to content compilation and website publishing.
- manuscript allows website creation with an emphasis in reproducibility and targeted to scientific and academic documents.

R

targets allows automatic functions execution and dependencies management between them.

Check current workflow state and execute only outdated targets.

File monitoring and code re-execution when change detection.

R

graph LR
  x3d474db92cf09724>"mensaje"]:::outdated ==> xc5ec810879cc40ee>"recorte"]:::outdated
    x3d474db92cf09724>"mensaje"]:::outdated ==> x32cb0d977e75588d>"elimino"]:::outdated
    x3d474db92cf09724>"mensaje"]:::outdated ==> x0dc39fa9e42347ba>"reflectancia"]:::outdated
    x3d474db92cf09724>"mensaje"]:::outdated ==> x0e71b645b3e50d0c>"script_descarga_py"]:::outdated
    x3d474db92cf09724>"mensaje"]:::outdated ==> x70dd0adf732b9ac4>"estado_descarga"]:::outdated
    xfabd587be49f2fed>"fecha"]:::outdated ==> x0dc39fa9e42347ba>"reflectancia"]:::outdated
    xfabd587be49f2fed>"fecha"]:::outdated ==> x38637a02f9b83fc8>"lab"]:::outdated
    x0e71b645b3e50d0c>"script_descarga_py"]:::outdated ==> x70dd0adf732b9ac4>"estado_descarga"]:::outdated
    x2eb57580dd338e28(["excel"]):::outdated ==> x1a91c1978c7a143b(["datos_lab"]):::outdated
    x38637a02f9b83fc8>"lab"]:::outdated ==> x1a91c1978c7a143b(["datos_lab"]):::outdated
    x3975d57dc4a04f5c>"descarga"]:::outdated ==> x0a08cea06a6d211f(["producto_zip"]):::outdated
    xe56f95f4237d1e66(["script_py"]):::outdated ==> x0a08cea06a6d211f(["producto_zip"]):::outdated
    xd2e55a6b497fb062(["fecha_descarga"]):::outdated ==> x4b150ba8dbe4203d(["recorte_tif"]):::outdated
    x0a08cea06a6d211f(["producto_zip"]):::outdated ==> x4b150ba8dbe4203d(["recorte_tif"]):::outdated
    xc5ec810879cc40ee>"recorte"]:::outdated ==> x4b150ba8dbe4203d(["recorte_tif"]):::outdated
    x29bd13377b9e6171>"archivo_excel"]:::outdated ==> x2eb57580dd338e28(["excel"]):::outdated
    x2eb57580dd338e28(["excel"]):::outdated ==> xd2e55a6b497fb062(["fecha_descarga"]):::outdated
    xfabd587be49f2fed>"fecha"]:::outdated ==> xd2e55a6b497fb062(["fecha_descarga"]):::outdated
    xd2e55a6b497fb062(["fecha_descarga"]):::outdated ==> xe56f95f4237d1e66(["script_py"]):::outdated
    x0e71b645b3e50d0c>"script_descarga_py"]:::outdated ==> xe56f95f4237d1e66(["script_py"]):::outdated
    x2eb57580dd338e28(["excel"]):::outdated ==> x75ae8feee719d1e2(["datos_gis"]):::outdated
    xd2e55a6b497fb062(["fecha_descarga"]):::outdated ==> x75ae8feee719d1e2(["datos_gis"]):::outdated
    x4b150ba8dbe4203d(["recorte_tif"]):::outdated ==> x75ae8feee719d1e2(["datos_gis"]):::outdated
    x0dc39fa9e42347ba>"reflectancia"]:::outdated ==> x75ae8feee719d1e2(["datos_gis"]):::outdated

  classDef outdated stroke:#FFC0CB,color:#FFFFFF,fill:#224289;
  classDef errored stroke:#FFC0CB,color:#FFFFFF,fill:#224289;
  classDef none stroke:#FFC0CB,color:#FFFFFF,fill:#224289;

R

renv execution environment management, package version and its dependencies.

Log file that allows environment reproducibility.

R

tidyverse with multiple packages for general purpose data processing and manipulation.

terra for geographic data processing and vector and raster reading.

corrr linear correlation coefficient calculation.

R

ggplot2 for basic plot creation (.png).

ggiraph for interactive plot creation (.html).

leaflet for interactive map creation (.html).

PYTHON

Copernicus Data Space

Collection
Processing level
Region of interest
Time range
Credentials

GIT

Version control management and simultaneous collaboration between project members.

github cloud storage service

branch per member, so each one works in a specific section without interfering with the remaining repository

pull request to request adding changes

merge to combine changes once checked and accepted

QUARTO

Combines code execution by programming language and narrative text to create a product in multiple formatted options
Offers a publishing platform for the output and to access it as a website

%%{
  init: {
    'themeVariables': {
      'edgeLabelBackground': '#224289',
      'edgeLabel': 'red'
    }
  }
}%%

flowchart LR
  s1[<span class="ant-design--code-filled"></span><br>scripts]:::e1 ==> q1[<span class="simple-icons--quarto"></span><br>quarto]:::e1

  s2[<span class="material-symbols--markdown"></span><br>markdown]:::e1 ===> q1

  s3[<span class="fe--document"></span><br>text]:::e1 ===> q1

  s4[<span class="file-icons--latex"></span>]:::e1 ==> q1

  q1 ==> h1[<span class="qlementine-icons--file-html-16"></span><br>html]:::e1

  h1 ==>|<b style='color:white'>quarto pub</b>| w1[<span class="mdi--web"></span><br>website]:::e1

  classDef e1 stroke:none,color:#FFFFFF,fill:none;

QUARTO

quarto manuscript is design for scientific document authoring, with emphasis in reproducibility, since it encourages the readers to explore processing scripts (notebooks).
Offers multiple static outputs (.pdf, .docx) that follow an specific template from a magazine.
quarto publish allows to deploy the website in Quarto Pub or GitHub Pages .
In combination with targets, plots/tables/maps are regenerated with new data input, or script modification, updating the results.

QUARTO

File and directories tree.

quarto_manuscript
├── bibliography
│   ├── ieee.csl
│   └── reference.bib
├── data
│   ├── laboratory.csv
│   └── reflectance.csv
├── plot
│   ├── boxplot.png
│   └── time_series.png
├── manuscript.qmd
├── notebooks
│   ├── plots.qmd
│   └── data_reading.qmd
├── _publish.yml
├── raster
├── scripts
│   ├── functions.R
│   └── support.R
├── vectors
├── _quarto.yml
└── _targets.R

QUARTO

manuscript.qmd

---
title: Research Project
author: Víctor Gauto
date: last modified
---

# Introducción

**Paraná River** has <i>water</i>.

````{r}
ggplot(data, aes(x, y)) +
  geom_point()
````

QUARTO

_quarto.yml

project:
  type: manuscript

manuscript:
  article: manuscrito.qmd
  notebooks:
    - notebooks/data_reading.qmd

format:
  html:
    lang: es
    include-in-header:
      - extras/favicon.html
    theme:
      - extras/my_style.scss
    toc: true
    code-link: true
    code-copy: true
    tbl-cap-location: margin
    fig-cap-location: bottom
    bibliography: bibliography/reference.bib
    csl: bibliography/ieee.csl
    html-math-method: katex

QUARTO

_publish.yml

- source: project
  quarto-pub:
    - id: ff90d76c-20c0-4210-8791-5d868ede4c50
      url: https://vhgauto.quarto.pub/gistaq-parana

Conclusion

The Project Research development allowed us to learn a new set of tools.

Future improvements

Rewrite functions used by targets.
- Define arguments clearly.
- Return descriptive messages during runtime and in case of errors.
- Incorporate website rendering.
Optimize satellite data download, avoiding to get the entire product.
- Google Earth Engine.
- rsi package.
Generate a .pdf version of the website for easy sharing.
Organice website visual features (colors, fonts, styles, margins) in the .scss file.
Use the full potential of quarto manuscript, so the results are created by the notebooks.

Thanks for your time

MS Víctor Gauto

victor.gauto@ca.frre.utn.edu.ar

Resources

Download

This presentation repository

Reproducible Manuscripts with Quarto - posit::conf(2023)

Quarto for Academics | Mine Çetinkaya-Rundel

Quarto | Get started

Quarto Manuscripts

The {targets} R package user manual

Introduction to renv

R for Data Science (2e)

ggiraph-book

Website repository

Quarto Extensions

Official repository for Citation Style Language (CSL) citation styles